Epidemiological investigation always play an important role in formulating preventing and control policies of any infectious disease and from this perspective molecular epidemiological background is of utmost importance for any virologist to chalk out better stampling policy of any viral disease. There are some infectious viral diseases of livestock that are prevalent in India viz., Foot-and-mouth disease, Infectious Bovine Rhinotracheitis, Blue Tongue, Rota viral diarrhoea, Rabies, Peste-des-petits ruminants and Classical swine fever that are responsible for causing serious economic loss in the livestock sector. This monograph has highlighted the several approaches for molecular epidemiological investigation of these diseases with the ultimate aim to prevent the damage to the economy contributed by the livestock sector to a developing nation like India.